ILRI Research Computing

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====== Snippy ======

Rapid haploid variant calling and core genome alignment.


===== Information =====

  * Version: 4.6.0
  * Added: July, 2023
  * Link: https://github.com/tseemann/snippy

===== Usage =====

See which versions are available:
<code>$ module avail snippy</code>

Load one version into your environment and run it:
<code>$ module load snippy/4.6.0
$ snippy</code>

**Note:** Please use the %%''--cpus''%% option to tell snippy how many CPUs it should use or else it will automatically use eight (8). This number should match the number of CPUs you requested in your SLURM batch allocation.

===== Installation ======

Notes from the sysadmin during installation:

<code>$ cd /tmp
$ git clone https://github.com/tseemann/snippy.git -b v4.6.0
$ cd snippy
$ grep -rh -oE "use Bio::.*$" bin/* binaries/* | sort -u | awk '{print $2}' | sed 's/;//'
Bio::SeqIO
Bio::Tools::GFF
$ cpanm -l perl5 Bio::SeqIO Bio::Tools::GFF
$ sudo mkdir -p /export/apps/snippy/4.6.0
$ sudo cp -r . /export/apps/snippy/4.6.0</code>

**Note 1:** Snippy only says that it requires "BioPerl", but the BioPerl distribution frowns upon requiring the entire distribution. Here I have attempted to guess which modules are needed by checking the actual Perl "use" statements.